Bacteriophage in Cheese Production: What Every Cheesemaker Needs to Know

Bacteriophage contamination is one of the most significant challenges facing cheese manufacturers worldwide. Whether you’re producing artisanal farmstead cheese or managing large-scale commercial operations, understanding bacteriophage in cheese production can mean the difference between consistent quality and costly production failures.

What is Bacteriophage?

Bacteriophages, commonly called “phages,” are viruses that specifically infect and destroy bacteria. In the context of cheese production, these microscopic parasites target the beneficial lactic acid bacteria (LAB) that are essential for proper fermentation and cheese development.

The term “bacteriophage” literally means “bacteria eater,” which accurately describes their devastating impact on starter cultures. A single phage particle can infect a bacterial cell, replicate inside it, and release hundreds of new phage particles when the cell bursts open. This process, known as lysis, can occur in as little as 30-60 minutes under optimal conditions.

Why Bacteriophages Matter in Cheese Production

Phages primarily target the key bacteria used in cheese making, including:

• Lactococcus lactis – the most common starter culture for many cheese varieties
• Streptococcus thermophilus – essential for mozzarella, yogurt, and Swiss-type cheeses
• Lactobacillus helveticus – critical for Parmesan, Grana Padano, and other hard Italian cheeses
• Lactobacillus delbrueckii – used in yogurt and some cheese productions

When bacteriophage in cheese facilities infects these cultures, the result is slow or incomplete acid development, leading to what producers call “dead vats” or “slow vats.” The economic impact can be substantial, with entire production runs potentially lost.

How Bacteriophages Propagate in Cheese Facilities

Understanding phage propagation is crucial for developing effective control strategies. Bacteriophages spread through cheese facilities via multiple pathways, creating a cycle of contamination that can persist for years if not properly managed.

Primary Sources of Phage Contamination

Raw Milk: Research indicates that approximately 10% of raw milk samples contain infectious phages, with concentrations ranging from 10¹ to 10⁴ phages per milliliter. Raw milk serves as a continuous source of new phage variants entering your facility.

Whey: This is arguably the most significant source of phage proliferation. During cheese production, phage concentrations can reach 10⁹ phages per milliliter of whey. When whey is handled, stored, or recycled, it creates numerous opportunities for phage dispersal throughout the facility.

Airborne Transmission: Studies dating back to the 1940s confirmed that phages become airborne through aerosols created during various production activities. Concentrations can reach 10⁸ plaque-forming units (PFU) per cubic meter of air, particularly near whey handling areas, drain systems, and vat-filling operations.

Equipment and Surfaces: Phages persist on inadequately cleaned equipment, particularly in areas that are difficult to sanitize such as:

• Gaskets and seals
• Vat agitators and paddles
• Drain systems and floor surfaces
• Pipework and transfer lines
• Bulk starter vessels and associated equipment

The Phage Multiplication Cycle

Once bacteriophage in cheese production finds its way into your starter culture, multiplication occurs rapidly. The process follows this pattern:

1. Attachment: The phage attaches to specific receptor sites on the bacterial cell surface
2. Injection: The phage injects its genetic material into the bacterial cell
3. Replication: The phage DNA commandeers the bacterial machinery to produce new phage particles
4. Assembly: New phage particles are assembled inside the bacterial cell
5. Lysis: The bacterial cell bursts, releasing 50-300 new phage particles
6. Repeat: Each new phage can infect another bacterial cell, creating exponential growth

The latent period (time from infection to lysis) for lactococcal phages is typically 30-60 minutes. This means that even a small number of phage particles entering your bulk starter can result in complete culture lysis before or during cheese making.

Persistence in the Environment

Bacteriophages are remarkably resilient. They can:

• Survive milk pasteurization temperatures in some cases
• Persist in brine solutions at concentrations up to 10⁸ PFU/ml
• Remain viable on surfaces for extended periods
• Withstand refrigeration and even freezing temperatures
• Survive in whey storage tanks and transfer systems

This environmental persistence explains why phage problems often recur in facilities even after implementing control measures.

How to Avoid Bacteriophage Contamination

Prevention is far more effective than attempting to eliminate established phage populations. A comprehensive phage control strategy requires multiple overlapping defenses—an approach similar to “hurdle technology” in food safety.

1. Aseptic Starter Propagation

Your bulk starter production system is your first line of defense. Modern aseptic systems should include:

Enclosed starter vessels with positive pressure systems to prevent airborne phage entry. The vessel should be designed to minimize headspace, and any air entering should be filtered through high-efficiency particulate air (HEPA) filters.

Dedicated starter rooms physically separated from cheese production areas. These rooms should maintain positive air pressure relative to adjacent areas and have dedicated ventilation systems that don’t share air with production zones.

Strict sanitation protocols for all starter-handling equipment. This includes complete CIP (clean-in-place) systems with proven effectiveness against phage contamination.

2. Culture Management Strategies

Multiple Culture Rotation: Never rely on a single starter strain. Implement a rotation system using 3-6 different phage-unrelated strains. This means the phages that attack strain A cannot infect strains B, C, or D. Even if phage contamination occurs, you can switch to an unaffected culture the next day.

Phage-Inhibitory Media: Some media formulations contain compounds like phosphate that can inhibit phage replication without affecting bacterial growth. Consult with your culture supplier about options.

Direct Vat Inoculation (DVI): Consider using frozen concentrated cultures added directly to the cheese vat, bypassing the bulk starter preparation step entirely. This eliminates the most vulnerable point in traditional starter systems.

3. Facility Design and Workflow

Physical Separation: Design your facility to prevent cross-contamination:

• Separate whey handling from milk reception areas
• Locate whey storage tanks away from production zones
• Use dedicated equipment for different culture systems
• Implement one-way workflow patterns to prevent backtracking

Air Quality Management: Install proper ventilation and air conditioning systems. Consider UV light systems in critical areas to reduce airborne phage concentrations. Maintain positive pressure in clean areas relative to potentially contaminated zones.

Minimize Aerosol Generation: Many common activities create phage-laden aerosols:

• Vat filling and whey removal
• High-pressure cleaning
• Transfer pump operations
• Drain system activities

Use covered systems where possible and schedule high-risk activities when starter preparation is complete.

4. Equipment Sanitation

Regular CIP Validation: Your cleaning-in-place systems must be validated to ensure complete phage removal. Pay special attention to:

• Complete drainage before cleaning
• Adequate contact time with sanitizers
• Proper chemical concentrations
• Temperature maintenance throughout cleaning cycles

Chlorination Programs: Chlorine-based sanitizers remain effective against phages when used at proper concentrations. However, balance this with food safety concerns about disinfection byproducts. Some European facilities are transitioning to peracetic acid as an alternative.

Equipment Inspection: Regularly inspect for:

• Pin holes in jacket systems
• Worn gaskets and seals
• Deposits in bulk starter vessels
• Dead legs in piping systems

5. Raw Material Management

Milk Quality Testing: While you can’t completely eliminate phages from raw milk, understanding your baseline contamination helps:

• Test incoming milk for phage presence when problems arise
• Track seasonal variations in phage levels
• Identify problematic milk suppliers if patterns emerge

Whey Handling: This is critical because whey is the primary phage reservoir:

• Never use equipment that handles whey to transport raw milk
• Implement thorough rinsing protocols for shared tankers
• Consider dedicated whey handling equipment
• Remove whey from the facility as quickly as possible
• Ensure complete drainage of whey lines after use

6. Monitoring and Early Detection

Implement a phage monitoring program in partnership with your culture supplier:

• Regular testing of bulk starters for phage contamination
• Activity tests to detect slow acid production
• Turbidity tests on bacterial isolates
• Environmental sampling in high-risk areas

Early detection allows you to switch cultures before significant production losses occur.

How to Eliminate Bacteriophage Once It’s in Your Facility

Despite best prevention efforts, phage contamination sometimes becomes established in cheese facilities. Elimination requires a systematic, aggressive approach combining immediate response with long-term environmental decontamination.

Immediate Response Actions

Culture Switching: The moment you detect phage contamination, immediately switch to a phage-unrelated culture strain. This is your fastest path to resuming normal production. Your culture supplier should have alternative strains available that the existing phages cannot attack.

Production Schedule Adjustment: Consider these tactical changes:

• Reduce bulk starter volumes to minimize exposure time
• Implement earlier renneting to reduce the time phages have to multiply before curd formation
• Increase inoculation rates to overwhelm low phage concentrations

Isolation: Identify and isolate the contamination source:

• Test bulk starters, whey, brine, and environmental samples
• Map the contamination zones in your facility
• Restrict movement of equipment and personnel from contaminated to clean areas

Deep Cleaning Protocols

Elimination requires cleaning beyond your normal CIP routines:

Complete System Shutdown: Schedule a production shutdown for thorough facility decontamination:

• Empty and clean all vats, tanks, and vessels
• Disassemble equipment to access hidden surfaces
• Remove and replace all gaskets and seals
• Clean or replace air filters
• Address floor drains and waste systems

Enhanced Chemical Treatments: Use stronger sanitizer concentrations and longer contact times than normal operations:

• Chlorine solutions at elevated concentrations
• Peracetic acid treatments for equipment that can handle it
• Hot caustic washes followed by acid rinses
• Consider overnight soaking of critical equipment

Physical Cleaning: Don’t rely solely on chemical treatments:

• Manual scrubbing of accessible surfaces
• High-pressure washing of walls, floors, and ceilings
• Steam cleaning of equipment surfaces
• Removal of biofilm from drain systems

Environmental Decontamination

Air System Treatment: Address airborne phages:

• Replace or thoroughly clean all HEPA filters
• Clean air handling ducts and vents
• Consider UV light installation in air systems
• Verify positive pressure differentials are maintained

Whey System Overhaul: Since whey is the primary phage reservoir:

• Clean all whey storage tanks and transfer lines
• Replace flexible hoses that can harbor phages
• Verify complete drainage of all whey piping
• Consider changing whey hauling schedules to prevent buildup

Surface Decontamination: Beyond equipment:

• Deep clean all walls, floors, and ceilings in production areas
• Pay attention to overhead structures, lights, and conduit
• Address areas around drains where phage aerosols settle
• Clean or replace floor mats and equipment wheels

Long-Term Control Measures

After initial elimination efforts:

Verification Testing: Confirm phage elimination through:

• Environmental sampling of previously contaminated areas
• Extended monitoring of starter culture performance
• Testing of first production batches using sensitive indicators

Preventive Maintenance Schedule: Implement regular:

• Deep cleaning cycles (monthly or quarterly)
• Equipment seal and gasket replacement
• Air filter changes
• Verification of CIP system effectiveness

Culture Rotation Commitment: Never return to single-culture dependence. Maintain a permanent rotation system even after phage problems are resolved.

Documentation and Training: Record:

• The contamination event and response actions taken
• Changes to procedures and equipment
• Staff training on phage prevention protocols
• Ongoing monitoring results

Working with Experts

Severe or persistent phage problems may require external expertise:

• Consult with your culture supplier’s technical support
• Consider engaging dairy microbiology consultants
• Partner with university research programs studying phage control
• Join industry groups to learn from others’ experiences

When to Consider Facility Modifications

If phage problems persist despite aggressive control measures, facility design issues may be at fault:

• Inadequate separation between whey and milk handling
• Poor ventilation system design
• Equipment that’s impossible to clean adequately
• Insufficient capacity for proper culture rotation

These situations may require capital investment in facility upgrades, but chronic phage problems often justify the expense through improved production consistency.

The Bottom Line on Bacteriophage Control

Bacteriophage in cheese production represents a persistent challenge, but it’s not insurmountable. Success requires understanding phage biology, implementing overlapping prevention strategies, maintaining vigilant monitoring, and responding decisively when contamination occurs.

The most successful cheese facilities share common characteristics:

• Multiple, phage-unrelated cultures in rotation
• Aseptic starter preparation systems
• Rigorous equipment sanitation programs
• Physical separation of high-risk activities
• Partnership with knowledgeable culture suppliers
• Commitment to ongoing monitoring and continuous improvement

Remember that phage control is an ongoing process, not a one-time fix. Environmental phages are ubiquitous in dairy environments, with new variants continuously entering through raw milk. The goal isn’t complete eradication—which is impossible—but rather maintaining phage concentrations below levels that impact production.

Modern cheese manufacturers using DairyCraftPro software can track starter performance metrics, document cleaning schedules, and maintain culture rotation records to support comprehensive phage control programs. By combining good manufacturing practices with systematic monitoring, you can minimize bacteriophage impact and maintain consistent, high-quality cheese production.

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References

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2. Queiroz, G. A., Santana, T. M., Monteiro-Batista, M. C., Orabona, G. M., Santana, V. V., Silva, E. O., Pimentel, T. C., Freitas, M. Q., & Raices, R. S. L. (2023). High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community. mSystems, 7(6), e00564-22. https://doi.org/10.1128/msystems.00564-22
3. Garneau, J. E., & Moineau, S. (2011). Bacteriophages of lactic acid bacteria and their impact on milk fermentations. Microbial Cell Factories, 10(Suppl 1), S20. https://doi.org/10.1186/1475-2859-10-S1-S20
4. Mahony, J., & van Sinderen, D. (2015). Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria. Annual Review of Food Science and Technology, 6, 521-540. https://doi.org/10.1146/annurev-food-041715-033322